Starting phenix.real_space_refine on Wed Mar 20 05:49:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2e_27833/03_2024/8e2e_27833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2e_27833/03_2024/8e2e_27833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2e_27833/03_2024/8e2e_27833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2e_27833/03_2024/8e2e_27833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2e_27833/03_2024/8e2e_27833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2e_27833/03_2024/8e2e_27833.pdb" } resolution = 1.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.134 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 8288 2.51 5 N 2182 2.21 5 O 2733 1.98 5 H 13332 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 2181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 2391": "OD1" <-> "OD2" Residue "A GLU 2658": "OE1" <-> "OE2" Residue "A PHE 2684": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 3199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 3345": "OE1" <-> "OE2" Residue "A ASP 3429": "OD1" <-> "OD2" Residue "B TYR 2181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2391": "OD1" <-> "OD2" Residue "B GLU 2658": "OE1" <-> "OE2" Residue "B PHE 2684": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 2845": "OE1" <-> "OE2" Residue "B GLU 2939": "OE1" <-> "OE2" Residue "B ASP 3090": "OD1" <-> "OD2" Residue "B TYR 3199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 3209": "OD1" <-> "OD2" Residue "B ASP 3343": "OD1" <-> "OD2" Residue "B GLU 3345": "OE1" <-> "OE2" Residue "B ASP 3429": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26633 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13128 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 827, 12953 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 35, 'TRANS': 791} Chain breaks: 14 Conformer: "B" Number of residues, atoms: 827, 12953 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 35, 'TRANS': 791} Chain breaks: 14 bond proxies already assigned to first conformer: 12880 Chain: "B" Number of atoms: 13128 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 827, 12953 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 35, 'TRANS': 791} Chain breaks: 14 Conformer: "B" Number of residues, atoms: 827, 12953 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 35, 'TRANS': 791} Chain breaks: 14 bond proxies already assigned to first conformer: 12880 Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 195 Classifications: {'water': 195} Link IDs: {None: 194} Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Classifications: {'water': 182} Link IDs: {None: 181} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N ACYS A2642 " occ=0.60 ... (20 atoms not shown) pdb=" HG BCYS A2642 " occ=0.40 residue: pdb=" N ASER A2703 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER A2703 " occ=0.50 residue: pdb=" N ASER A2725 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER A2725 " occ=0.50 residue: pdb=" N ATHR A2748 " occ=0.50 ... (26 atoms not shown) pdb="HG23BTHR A2748 " occ=0.50 residue: pdb=" N AVAL A2753 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL A2753 " occ=0.50 residue: pdb=" N ASER A2809 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER A2809 " occ=0.50 residue: pdb=" N ASER A2820 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER A2820 " occ=0.50 residue: pdb=" N ATHR A3074 " occ=0.60 ... (26 atoms not shown) pdb="HG23BTHR A3074 " occ=0.40 residue: pdb=" N AILE A3118 " occ=0.70 ... (36 atoms not shown) pdb="HD13BILE A3118 " occ=0.30 residue: pdb=" N AVAL A3257 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL A3257 " occ=0.50 residue: pdb=" N ASER A3368 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER A3368 " occ=0.50 residue: pdb=" N AILE A3392 " occ=0.50 ... (36 atoms not shown) pdb="HD13BILE A3392 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 20.89, per 1000 atoms: 0.78 Number of scatterers: 26633 At special positions: 0 Unit cell: (104.72, 168.08, 84.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 2733 8.00 N 2182 7.00 C 8288 6.00 H 13332 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.00 Conformation dependent library (CDL) restraints added in 5.4 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 4 sheets defined 66.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 2141 through 2147 Processing helix chain 'A' and resid 2148 through 2150 No H-bonds generated for 'chain 'A' and resid 2148 through 2150' Processing helix chain 'A' and resid 2164 through 2181 Processing helix chain 'A' and resid 2199 through 2204 removed outlier: 4.283A pdb=" N PHE A2203 " --> pdb=" O GLN A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2326 through 2342 Processing helix chain 'A' and resid 2347 through 2365 removed outlier: 3.616A pdb=" N PHE A2353 " --> pdb=" O ASP A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2375 Processing helix chain 'A' and resid 2376 through 2389 removed outlier: 3.553A pdb=" N LEU A2387 " --> pdb=" O LEU A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2400 through 2420 removed outlier: 3.602A pdb=" N ALA A2404 " --> pdb=" O GLY A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2635 through 2649 Processing helix chain 'A' and resid 2656 through 2669 Processing helix chain 'A' and resid 2697 through 2711 Processing helix chain 'A' and resid 2715 through 2731 Processing helix chain 'A' and resid 2747 through 2754 Processing helix chain 'A' and resid 2755 through 2767 removed outlier: 4.186A pdb=" N ILE A2759 " --> pdb=" O ASP A2755 " (cutoff:3.500A) Processing helix chain 'A' and resid 2781 through 2802 removed outlier: 4.414A pdb=" N ALA A2785 " --> pdb=" O VAL A2781 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A2802 " --> pdb=" O VAL A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2804 through 2821 removed outlier: 3.997A pdb=" N PHE A2808 " --> pdb=" O CYS A2804 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2829 Processing helix chain 'A' and resid 2832 through 2844 Processing helix chain 'A' and resid 2852 through 2873 Processing helix chain 'A' and resid 2915 through 2931 removed outlier: 3.749A pdb=" N GLN A2931 " --> pdb=" O ASN A2927 " (cutoff:3.500A) Processing helix chain 'A' and resid 2980 through 2987 Processing helix chain 'A' and resid 2987 through 3000 Processing helix chain 'A' and resid 3031 through 3047 Processing helix chain 'A' and resid 3049 through 3063 removed outlier: 3.644A pdb=" N MET A3053 " --> pdb=" O THR A3049 " (cutoff:3.500A) Proline residue: A3056 - end of helix Processing helix chain 'A' and resid 3064 through 3068 Processing helix chain 'A' and resid 3078 through 3089 Processing helix chain 'A' and resid 3091 through 3101 Processing helix chain 'A' and resid 3102 through 3117 Processing helix chain 'A' and resid 3124 through 3133 Processing helix chain 'A' and resid 3164 through 3167 Processing helix chain 'A' and resid 3179 through 3184 removed outlier: 3.940A pdb=" N LEU A3183 " --> pdb=" O ALA A3179 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A3184 " --> pdb=" O GLU A3180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3179 through 3184' Processing helix chain 'A' and resid 3229 through 3235 removed outlier: 4.022A pdb=" N LEU A3232 " --> pdb=" O LEU A3229 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA A3233 " --> pdb=" O ALA A3230 " (cutoff:3.500A) Processing helix chain 'A' and resid 3305 through 3309 removed outlier: 3.626A pdb=" N SER A3309 " --> pdb=" O THR A3306 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3326 Processing helix chain 'A' and resid 3327 through 3340 removed outlier: 3.679A pdb=" N LEU A3331 " --> pdb=" O SER A3327 " (cutoff:3.500A) Processing helix chain 'A' and resid 3341 through 3343 No H-bonds generated for 'chain 'A' and resid 3341 through 3343' Processing helix chain 'A' and resid 3344 through 3353 Processing helix chain 'A' and resid 3357 through 3367 Processing helix chain 'A' and resid 3374 through 3388 removed outlier: 3.658A pdb=" N ILE A3378 " --> pdb=" O HIS A3374 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3402 Processing helix chain 'A' and resid 3428 through 3441 Processing helix chain 'A' and resid 3445 through 3466 Processing helix chain 'A' and resid 3484 through 3488 Processing helix chain 'A' and resid 3490 through 3503 Processing helix chain 'B' and resid 2142 through 2147 Processing helix chain 'B' and resid 2148 through 2150 No H-bonds generated for 'chain 'B' and resid 2148 through 2150' Processing helix chain 'B' and resid 2164 through 2181 Processing helix chain 'B' and resid 2199 through 2204 removed outlier: 4.283A pdb=" N PHE B2203 " --> pdb=" O GLN B2200 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2342 Processing helix chain 'B' and resid 2347 through 2365 removed outlier: 3.617A pdb=" N PHE B2353 " --> pdb=" O ASP B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2370 through 2375 Processing helix chain 'B' and resid 2376 through 2389 removed outlier: 3.552A pdb=" N LEU B2387 " --> pdb=" O LEU B2383 " (cutoff:3.500A) Processing helix chain 'B' and resid 2400 through 2420 removed outlier: 3.601A pdb=" N ALA B2404 " --> pdb=" O GLY B2400 " (cutoff:3.500A) Processing helix chain 'B' and resid 2635 through 2649 Processing helix chain 'B' and resid 2656 through 2669 Processing helix chain 'B' and resid 2697 through 2711 Processing helix chain 'B' and resid 2715 through 2731 Processing helix chain 'B' and resid 2747 through 2754 Processing helix chain 'B' and resid 2755 through 2767 removed outlier: 4.187A pdb=" N ILE B2759 " --> pdb=" O ASP B2755 " (cutoff:3.500A) Processing helix chain 'B' and resid 2781 through 2802 removed outlier: 4.412A pdb=" N ALA B2785 " --> pdb=" O VAL B2781 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B2802 " --> pdb=" O VAL B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2804 through 2821 removed outlier: 3.997A pdb=" N PHE B2808 " --> pdb=" O CYS B2804 " (cutoff:3.500A) Processing helix chain 'B' and resid 2824 through 2829 Processing helix chain 'B' and resid 2832 through 2844 Processing helix chain 'B' and resid 2852 through 2873 Processing helix chain 'B' and resid 2915 through 2931 removed outlier: 3.749A pdb=" N GLN B2931 " --> pdb=" O ASN B2927 " (cutoff:3.500A) Processing helix chain 'B' and resid 2980 through 2987 Processing helix chain 'B' and resid 2987 through 3000 Processing helix chain 'B' and resid 3031 through 3047 Processing helix chain 'B' and resid 3049 through 3063 removed outlier: 3.645A pdb=" N MET B3053 " --> pdb=" O THR B3049 " (cutoff:3.500A) Proline residue: B3056 - end of helix Processing helix chain 'B' and resid 3064 through 3068 Processing helix chain 'B' and resid 3078 through 3089 Processing helix chain 'B' and resid 3091 through 3101 Processing helix chain 'B' and resid 3102 through 3117 Processing helix chain 'B' and resid 3124 through 3133 Processing helix chain 'B' and resid 3164 through 3167 Processing helix chain 'B' and resid 3179 through 3184 removed outlier: 3.942A pdb=" N LEU B3183 " --> pdb=" O ALA B3179 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B3184 " --> pdb=" O GLU B3180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3179 through 3184' Processing helix chain 'B' and resid 3229 through 3235 removed outlier: 3.957A pdb=" N LEU B3232 " --> pdb=" O LEU B3229 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA B3233 " --> pdb=" O ALA B3230 " (cutoff:3.500A) Processing helix chain 'B' and resid 3305 through 3309 removed outlier: 3.645A pdb=" N SER B3309 " --> pdb=" O THR B3306 " (cutoff:3.500A) Processing helix chain 'B' and resid 3322 through 3326 Processing helix chain 'B' and resid 3327 through 3340 removed outlier: 3.677A pdb=" N LEU B3331 " --> pdb=" O SER B3327 " (cutoff:3.500A) Processing helix chain 'B' and resid 3341 through 3343 No H-bonds generated for 'chain 'B' and resid 3341 through 3343' Processing helix chain 'B' and resid 3344 through 3353 Processing helix chain 'B' and resid 3357 through 3367 Processing helix chain 'B' and resid 3374 through 3388 removed outlier: 3.659A pdb=" N ILE B3378 " --> pdb=" O HIS B3374 " (cutoff:3.500A) Processing helix chain 'B' and resid 3389 through 3402 Processing helix chain 'B' and resid 3428 through 3441 Processing helix chain 'B' and resid 3445 through 3466 Processing helix chain 'B' and resid 3484 through 3488 Processing helix chain 'B' and resid 3490 through 3503 Processing sheet with id=AA1, first strand: chain 'A' and resid 2877 through 2879 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2877 through 2879 current: chain 'A' and resid 3251 through 3252 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 2941 through 2943 removed outlier: 5.328A pdb=" N ALA A2978 " --> pdb=" O LEU A2934 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2877 through 2879 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2877 through 2879 current: chain 'B' and resid 3251 through 3252 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 2941 through 2943 removed outlier: 5.325A pdb=" N ALA B2978 " --> pdb=" O LEU B2934 " (cutoff:3.500A) 737 hydrogen bonds defined for protein. 2177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.33 Time building geometry restraints manager: 26.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13288 1.03 - 1.23: 421 1.23 - 1.43: 4862 1.43 - 1.62: 7785 1.62 - 1.82: 152 Bond restraints: 26508 Sorted by residual: bond pdb=" CG1BILE A3392 " pdb=" CD1BILE A3392 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.32e+00 bond pdb=" CG1BILE B3392 " pdb=" CD1BILE B3392 " ideal model delta sigma weight residual 1.513 1.420 0.093 3.90e-02 6.57e+02 5.63e+00 bond pdb=" CE LYS B2876 " pdb=" NZ LYS B2876 " ideal model delta sigma weight residual 1.489 1.425 0.064 3.00e-02 1.11e+03 4.56e+00 bond pdb=" CB MET B2638 " pdb=" CG MET B2638 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" CB MET A2638 " pdb=" CG MET A2638 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.16e+00 ... (remaining 26503 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.60: 228 104.60 - 112.01: 31703 112.01 - 119.42: 6308 119.42 - 126.83: 9683 126.83 - 134.23: 204 Bond angle restraints: 48126 Sorted by residual: angle pdb=" CA VAL A2388 " pdb=" C VAL A2388 " pdb=" N GLY A2389 " ideal model delta sigma weight residual 116.60 120.34 -3.74 1.45e+00 4.76e-01 6.66e+00 angle pdb=" CA VAL B2388 " pdb=" C VAL B2388 " pdb=" N GLY B2389 " ideal model delta sigma weight residual 116.60 120.29 -3.69 1.45e+00 4.76e-01 6.46e+00 angle pdb=" N ALA B3353 " pdb=" CA ALA B3353 " pdb=" C ALA B3353 " ideal model delta sigma weight residual 109.81 115.04 -5.23 2.21e+00 2.05e-01 5.60e+00 angle pdb=" N ALA A3353 " pdb=" CA ALA A3353 " pdb=" C ALA A3353 " ideal model delta sigma weight residual 109.81 115.01 -5.20 2.21e+00 2.05e-01 5.53e+00 angle pdb=" CA TRP A2710 " pdb=" CB TRP A2710 " pdb=" CG TRP A2710 " ideal model delta sigma weight residual 113.60 117.88 -4.28 1.90e+00 2.77e-01 5.07e+00 ... (remaining 48121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 11348 17.61 - 35.22: 751 35.22 - 52.82: 268 52.82 - 70.43: 62 70.43 - 88.04: 19 Dihedral angle restraints: 12448 sinusoidal: 6840 harmonic: 5608 Sorted by residual: dihedral pdb=" CA PHE B3420 " pdb=" C PHE B3420 " pdb=" N GLY B3421 " pdb=" CA GLY B3421 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA PHE A3420 " pdb=" C PHE A3420 " pdb=" N GLY A3421 " pdb=" CA GLY A3421 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ARG B2366 " pdb=" C ARG B2366 " pdb=" N PRO B2367 " pdb=" CA PRO B2367 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 12445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1127 0.028 - 0.055: 693 0.055 - 0.083: 286 0.083 - 0.111: 94 0.111 - 0.138: 36 Chirality restraints: 2236 Sorted by residual: chirality pdb=" CA BVAL B3257 " pdb=" N BVAL B3257 " pdb=" C BVAL B3257 " pdb=" CB BVAL B3257 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CB THR B2368 " pdb=" CA THR B2368 " pdb=" OG1 THR B2368 " pdb=" CG2 THR B2368 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA BVAL A3257 " pdb=" N BVAL A3257 " pdb=" C BVAL A3257 " pdb=" CB BVAL A3257 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 2233 not shown) Planarity restraints: 3820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A2830 " 0.010 2.00e-02 2.50e+03 1.87e-02 5.25e+00 pdb=" CD GLN A2830 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN A2830 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN A2830 " 0.008 2.00e-02 2.50e+03 pdb="HE21 GLN A2830 " 0.006 2.00e-02 2.50e+03 pdb="HE22 GLN A2830 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B3353 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO B3354 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B3354 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B3354 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A3353 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A3354 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A3354 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A3354 " -0.023 5.00e-02 4.00e+02 ... (remaining 3817 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1266 2.15 - 2.76: 53172 2.76 - 3.37: 86227 3.37 - 3.99: 112117 3.99 - 4.60: 171956 Nonbonded interactions: 424738 Sorted by model distance: nonbonded pdb=" OE1 GLN B2200 " pdb=" H GLN B2200 " model vdw 1.532 1.850 nonbonded pdb=" OE1 GLN A2200 " pdb=" H GLN A2200 " model vdw 1.533 1.850 nonbonded pdb=" HH TYR A2870 " pdb=" OD1 ASP A2916 " model vdw 1.574 1.850 nonbonded pdb=" HH TYR B2870 " pdb=" OD1 ASP B2916 " model vdw 1.575 1.850 nonbonded pdb=" OE1 GLU B2658 " pdb=" H GLU B2658 " model vdw 1.600 1.850 ... (remaining 424733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2141 through 2641 or resid 2644 through 2702 or resid 2705 \ through 2724 or resid 2727 through 2747 or resid 2750 through 2752 or resid 275 \ 5 through 2808 or resid 2811 through 2819 or resid 2822 through 3073 or resid 30 \ 76 through 3117 or resid 3120 through 3256 or resid 3259 through 3367 or resid 3 \ 369 through 3391 or resid 3394 through 3503)) selection = (chain 'B' and (resid 2141 through 2641 or resid 2644 through 2702 or resid 2705 \ through 2724 or resid 2727 through 2747 or resid 2750 through 2752 or resid 275 \ 5 through 2808 or resid 2811 through 2819 or resid 2822 through 3073 or resid 30 \ 76 through 3117 or resid 3120 through 3256 or resid 3259 through 3367 or resid 3 \ 369 through 3391 or resid 3394 through 3503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.570 Extract box with map and model: 24.180 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 106.790 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 13176 Z= 0.436 Angle : 0.736 6.441 17962 Z= 0.399 Chirality : 0.043 0.138 2236 Planarity : 0.005 0.058 2218 Dihedral : 14.151 88.038 4734 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.48 % Allowed : 10.18 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 1666 helix: -0.47 (0.14), residues: 1050 sheet: -0.82 (0.46), residues: 106 loop : -0.18 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A2710 HIS 0.011 0.002 HIS B2325 PHE 0.019 0.003 PHE A2643 TYR 0.013 0.002 TYR B3436 ARG 0.017 0.001 ARG A3391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 2.107 Fit side-chains revert: symmetry clash REVERT: A 2167 MET cc_start: 0.7059 (tpt) cc_final: 0.6696 (tpt) REVERT: B 2167 MET cc_start: 0.7025 (tpt) cc_final: 0.6682 (tpt) REVERT: B 3345 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7359 (tm-30) outliers start: 20 outliers final: 17 residues processed: 177 average time/residue: 2.4917 time to fit residues: 487.8890 Evaluate side-chains 177 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3208 CYS Chi-restraints excluded: chain A residue 3232 LEU Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3375 SER Chi-restraints excluded: chain A residue 3407 SER Chi-restraints excluded: chain A residue 3441 THR Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3232 LEU Chi-restraints excluded: chain B residue 3345 GLU Chi-restraints excluded: chain B residue 3355 THR Chi-restraints excluded: chain B residue 3375 SER Chi-restraints excluded: chain B residue 3407 SER Chi-restraints excluded: chain B residue 3441 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2205 ASN A2698 GLN A2787 GLN ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2830 GLN A3069 GLN A3268 GLN B2205 ASN B2787 GLN ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2830 GLN B3069 GLN B3226 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13176 Z= 0.278 Angle : 0.613 6.070 17962 Z= 0.321 Chirality : 0.038 0.142 2236 Planarity : 0.004 0.050 2218 Dihedral : 6.512 92.546 1788 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.68 % Allowed : 9.57 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1666 helix: 1.03 (0.15), residues: 1054 sheet: -0.37 (0.46), residues: 104 loop : 0.57 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B2710 HIS 0.007 0.001 HIS B3161 PHE 0.014 0.002 PHE B3084 TYR 0.009 0.001 TYR B3484 ARG 0.005 0.001 ARG A3391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 2.343 Fit side-chains REVERT: A 2814 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8590 (mtpt) REVERT: A 2827 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: B 2690 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7895 (mmm160) REVERT: B 2814 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8730 (mtpt) outliers start: 23 outliers final: 13 residues processed: 180 average time/residue: 2.5973 time to fit residues: 516.5720 Evaluate side-chains 171 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2814 LYS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3232 LEU Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3441 THR Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2690 ARG Chi-restraints excluded: chain B residue 2814 LYS Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3232 LEU Chi-restraints excluded: chain B residue 3345 GLU Chi-restraints excluded: chain B residue 3355 THR Chi-restraints excluded: chain B residue 3441 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2205 ASN ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13176 Z= 0.247 Angle : 0.580 5.555 17962 Z= 0.303 Chirality : 0.037 0.141 2236 Planarity : 0.004 0.046 2218 Dihedral : 6.087 92.761 1779 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.82 % Allowed : 9.50 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1666 helix: 1.65 (0.16), residues: 1046 sheet: -0.09 (0.47), residues: 104 loop : 0.85 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B2710 HIS 0.006 0.001 HIS B3161 PHE 0.013 0.002 PHE B3084 TYR 0.008 0.001 TYR A3436 ARG 0.004 0.000 ARG A3391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 2.337 Fit side-chains revert: symmetry clash REVERT: A 2167 MET cc_start: 0.6956 (tpt) cc_final: 0.6686 (tpt) REVERT: A 2360 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7932 (mmm160) REVERT: A 2690 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7782 (mmm160) REVERT: A 2827 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: A 2876 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7707 (mttt) REVERT: B 2167 MET cc_start: 0.6933 (tpt) cc_final: 0.6673 (tpt) REVERT: B 2690 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7887 (mmm160) outliers start: 25 outliers final: 18 residues processed: 171 average time/residue: 2.6687 time to fit residues: 504.4967 Evaluate side-chains 171 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2638 MET Chi-restraints excluded: chain A residue 2690 ARG Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3231 SER Chi-restraints excluded: chain A residue 3232 LEU Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3441 THR Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2690 ARG Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3231 SER Chi-restraints excluded: chain B residue 3232 LEU Chi-restraints excluded: chain B residue 3248 VAL Chi-restraints excluded: chain B residue 3345 GLU Chi-restraints excluded: chain B residue 3355 THR Chi-restraints excluded: chain B residue 3441 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2988 GLN ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13176 Z= 0.304 Angle : 0.615 5.423 17962 Z= 0.323 Chirality : 0.039 0.143 2236 Planarity : 0.004 0.043 2218 Dihedral : 6.164 97.038 1779 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.02 % Allowed : 9.37 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.20), residues: 1666 helix: 1.67 (0.16), residues: 1046 sheet: 0.11 (0.47), residues: 104 loop : 0.90 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2710 HIS 0.007 0.002 HIS B3161 PHE 0.016 0.002 PHE B3084 TYR 0.009 0.001 TYR B3484 ARG 0.006 0.001 ARG B3391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2360 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7929 (mmm160) REVERT: A 2690 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7790 (mmm160) REVERT: A 2814 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8590 (mtpt) REVERT: A 2827 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: B 2690 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7893 (mmm160) REVERT: B 2814 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8705 (mtpt) REVERT: B 2827 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7909 (tm-30) outliers start: 28 outliers final: 20 residues processed: 176 average time/residue: 2.7734 time to fit residues: 536.3163 Evaluate side-chains 177 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2690 ARG Chi-restraints excluded: chain A residue 2795 ARG Chi-restraints excluded: chain A residue 2814 LYS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3231 SER Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3441 THR Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2690 ARG Chi-restraints excluded: chain B residue 2795 ARG Chi-restraints excluded: chain B residue 2814 LYS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2988 GLN Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3231 SER Chi-restraints excluded: chain B residue 3248 VAL Chi-restraints excluded: chain B residue 3345 GLU Chi-restraints excluded: chain B residue 3355 THR Chi-restraints excluded: chain B residue 3441 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 142 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13176 Z= 0.258 Angle : 0.581 5.336 17962 Z= 0.304 Chirality : 0.038 0.141 2236 Planarity : 0.004 0.041 2218 Dihedral : 5.837 95.049 1775 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.09 % Allowed : 9.16 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.20), residues: 1666 helix: 1.82 (0.16), residues: 1048 sheet: 0.16 (0.47), residues: 104 loop : 0.97 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2710 HIS 0.006 0.001 HIS B3161 PHE 0.013 0.002 PHE A2643 TYR 0.008 0.001 TYR B3484 ARG 0.010 0.001 ARG A3391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2360 ARG cc_start: 0.8159 (mmm160) cc_final: 0.7938 (mmm160) REVERT: A 2690 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7803 (mmm160) REVERT: A 2814 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8588 (mtpt) REVERT: A 2827 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: B 2690 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7887 (mmm160) REVERT: B 2814 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8718 (mtpt) REVERT: B 2827 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7910 (tm-30) outliers start: 29 outliers final: 20 residues processed: 177 average time/residue: 2.6902 time to fit residues: 524.5934 Evaluate side-chains 176 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2690 ARG Chi-restraints excluded: chain A residue 2814 LYS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3231 SER Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3276 SER Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3441 THR Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2690 ARG Chi-restraints excluded: chain B residue 2795 ARG Chi-restraints excluded: chain B residue 2814 LYS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3231 SER Chi-restraints excluded: chain B residue 3248 VAL Chi-restraints excluded: chain B residue 3276 SER Chi-restraints excluded: chain B residue 3345 GLU Chi-restraints excluded: chain B residue 3355 THR Chi-restraints excluded: chain B residue 3441 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2989 GLN A2993 GLN ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13176 Z= 0.338 Angle : 0.634 5.276 17962 Z= 0.335 Chirality : 0.040 0.143 2236 Planarity : 0.005 0.042 2218 Dihedral : 5.961 98.265 1775 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.36 % Allowed : 8.89 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.20), residues: 1666 helix: 1.67 (0.15), residues: 1046 sheet: 0.27 (0.47), residues: 104 loop : 0.94 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2710 HIS 0.007 0.002 HIS B3161 PHE 0.017 0.002 PHE A2643 TYR 0.009 0.002 TYR A3436 ARG 0.006 0.001 ARG B3391 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2690 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7809 (mmm160) REVERT: A 2814 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8594 (mtpt) REVERT: A 2827 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: B 2690 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7895 (mmm160) REVERT: B 2814 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8724 (mtpt) REVERT: B 2827 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7918 (tm-30) outliers start: 33 outliers final: 25 residues processed: 179 average time/residue: 2.6556 time to fit residues: 523.7408 Evaluate side-chains 182 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2638 MET Chi-restraints excluded: chain A residue 2690 ARG Chi-restraints excluded: chain A residue 2795 ARG Chi-restraints excluded: chain A residue 2814 LYS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3231 SER Chi-restraints excluded: chain A residue 3232 LEU Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3276 SER Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain A residue 3355 THR Chi-restraints excluded: chain A residue 3441 THR Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2690 ARG Chi-restraints excluded: chain B residue 2795 ARG Chi-restraints excluded: chain B residue 2814 LYS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2988 GLN Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3231 SER Chi-restraints excluded: chain B residue 3232 LEU Chi-restraints excluded: chain B residue 3248 VAL Chi-restraints excluded: chain B residue 3276 SER Chi-restraints excluded: chain B residue 3345 GLU Chi-restraints excluded: chain B residue 3355 THR Chi-restraints excluded: chain B residue 3441 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2363 ASN ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2363 ASN ** B2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13176 Z= 0.209 Angle : 0.546 5.205 17962 Z= 0.283 Chirality : 0.037 0.141 2236 Planarity : 0.004 0.036 2218 Dihedral : 5.673 91.822 1775 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.89 % Allowed : 9.57 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.21), residues: 1666 helix: 2.04 (0.16), residues: 1048 sheet: 0.21 (0.47), residues: 104 loop : 1.03 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2710 HIS 0.005 0.001 HIS A3161 PHE 0.011 0.002 PHE A2643 TYR 0.006 0.001 TYR A3484 ARG 0.010 0.001 ARG B3391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2360 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7913 (mmm160) REVERT: A 2814 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8599 (mtpt) REVERT: A 2827 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: B 2814 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8728 (mtpt) REVERT: B 2827 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7910 (tm-30) outliers start: 26 outliers final: 16 residues processed: 177 average time/residue: 2.7506 time to fit residues: 535.7947 Evaluate side-chains 173 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2795 ARG Chi-restraints excluded: chain A residue 2814 LYS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3231 SER Chi-restraints excluded: chain A residue 3232 LEU Chi-restraints excluded: chain A residue 3276 SER Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2795 ARG Chi-restraints excluded: chain B residue 2814 LYS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2988 GLN Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3231 SER Chi-restraints excluded: chain B residue 3232 LEU Chi-restraints excluded: chain B residue 3276 SER Chi-restraints excluded: chain B residue 3345 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2830 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13176 Z= 0.235 Angle : 0.564 5.187 17962 Z= 0.294 Chirality : 0.037 0.141 2236 Planarity : 0.004 0.036 2218 Dihedral : 5.638 92.652 1771 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.75 % Allowed : 9.97 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.21), residues: 1666 helix: 2.00 (0.16), residues: 1048 sheet: 0.22 (0.47), residues: 104 loop : 1.04 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2710 HIS 0.005 0.001 HIS B3161 PHE 0.014 0.002 PHE B3084 TYR 0.007 0.001 TYR B2870 ARG 0.004 0.000 ARG B3391 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2360 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7912 (mmm160) REVERT: A 2814 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8594 (mtpt) REVERT: A 2827 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: B 2814 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8725 (mtpt) REVERT: B 2827 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7924 (tm-30) outliers start: 24 outliers final: 19 residues processed: 174 average time/residue: 2.6206 time to fit residues: 503.7790 Evaluate side-chains 180 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2795 ARG Chi-restraints excluded: chain A residue 2814 LYS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3231 SER Chi-restraints excluded: chain A residue 3232 LEU Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3276 SER Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2795 ARG Chi-restraints excluded: chain B residue 2814 LYS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2988 GLN Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3231 SER Chi-restraints excluded: chain B residue 3232 LEU Chi-restraints excluded: chain B residue 3248 VAL Chi-restraints excluded: chain B residue 3276 SER Chi-restraints excluded: chain B residue 3345 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2363 ASN B2363 ASN B2830 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13176 Z= 0.182 Angle : 0.524 5.086 17962 Z= 0.270 Chirality : 0.036 0.139 2236 Planarity : 0.004 0.037 2218 Dihedral : 5.438 86.249 1771 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.42 % Allowed : 10.65 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.21), residues: 1666 helix: 2.23 (0.16), residues: 1048 sheet: 0.17 (0.47), residues: 104 loop : 1.12 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B2710 HIS 0.004 0.001 HIS A3161 PHE 0.011 0.001 PHE A2643 TYR 0.005 0.001 TYR A3484 ARG 0.011 0.000 ARG B3391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2360 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7911 (mmm160) REVERT: A 2814 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8593 (mtpt) REVERT: A 2827 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: A 2876 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7502 (mmtt) REVERT: B 2814 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8722 (mtpt) REVERT: B 2827 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7935 (tm-30) outliers start: 19 outliers final: 11 residues processed: 179 average time/residue: 2.5783 time to fit residues: 509.9102 Evaluate side-chains 172 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2814 LYS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3232 LEU Chi-restraints excluded: chain A residue 3276 SER Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2814 LYS Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3232 LEU Chi-restraints excluded: chain B residue 3276 SER Chi-restraints excluded: chain B residue 3345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2363 ASN A3226 GLN B2363 ASN B2830 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13176 Z= 0.286 Angle : 0.602 5.180 17962 Z= 0.315 Chirality : 0.039 0.142 2236 Planarity : 0.004 0.044 2218 Dihedral : 5.700 94.586 1771 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.35 % Allowed : 10.51 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.20), residues: 1666 helix: 1.94 (0.16), residues: 1046 sheet: 0.27 (0.48), residues: 104 loop : 1.02 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A2710 HIS 0.006 0.001 HIS B3161 PHE 0.016 0.002 PHE B3084 TYR 0.010 0.001 TYR B3484 ARG 0.016 0.001 ARG B3391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2360 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7901 (mmm160) REVERT: A 2814 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8616 (mtpt) REVERT: A 2827 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: A 2876 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7549 (mmtt) REVERT: B 2814 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8742 (mtpt) REVERT: B 2827 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7942 (tm-30) outliers start: 18 outliers final: 12 residues processed: 167 average time/residue: 2.6387 time to fit residues: 486.0317 Evaluate side-chains 171 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 THR Chi-restraints excluded: chain A residue 2814 LYS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2988 GLN Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3232 LEU Chi-restraints excluded: chain A residue 3276 SER Chi-restraints excluded: chain A residue 3345 GLU Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2814 LYS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 3030 ILE Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3232 LEU Chi-restraints excluded: chain B residue 3276 SER Chi-restraints excluded: chain B residue 3345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2689 ASN B2363 ASN B2689 ASN B2830 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111929 restraints weight = 102165.127| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.02 r_work: 0.3133 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13176 Z= 0.289 Angle : 0.603 5.151 17962 Z= 0.316 Chirality : 0.039 0.141 2236 Planarity : 0.004 0.041 2218 Dihedral : 5.731 95.389 1771 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.48 % Allowed : 10.31 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.20), residues: 1666 helix: 1.88 (0.16), residues: 1046 sheet: 0.30 (0.48), residues: 104 loop : 1.00 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A2710 HIS 0.006 0.001 HIS B3161 PHE 0.014 0.002 PHE A2643 TYR 0.008 0.001 TYR B3484 ARG 0.007 0.001 ARG B3391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10189.08 seconds wall clock time: 179 minutes 8.66 seconds (10748.66 seconds total)